+Open data
-Basic information
Entry | Database: PDB / ID: 1cr7 | |||||||||
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Title | PEANUT LECTIN-LACTOSE COMPLEX MONOCLINIC FORM | |||||||||
Components | LECTIN | |||||||||
Keywords | SUGAR BINDING PROTEIN / LECTIN / LEGUME LECTIN / OPEN QUATERNARY STRUCTURE / MONOCLINIC FORM / ACIDIC PH / LACTOSE | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Arachis hypogaea (peanut) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | Ravishankar, R. / Suguna, K. / Surolia, A. / Vijayan, M. | |||||||||
Citation | Journal: Proteins / Year: 2001 Title: Crystal structures of the peanut lectin-lactose complex at acidic pH: retention of unusual quaternary structure, empty and carbohydrate bound combining sites, molecular mimicry and crystal ...Title: Crystal structures of the peanut lectin-lactose complex at acidic pH: retention of unusual quaternary structure, empty and carbohydrate bound combining sites, molecular mimicry and crystal packing directed by interactions at the combining site. Authors: Ravishankar, R. / Thomas, C.J. / Suguna, K. / Surolia, A. / Vijayan, M. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Structures of the Complexes of Peanut Lectin with Methyl-Beta-Galactose and N- Acetyllactosamine and a Comparative Study of Carbohydrate Binding in Gal/ Galnac-Specific Legume Lectins Authors: Ravishankar, R. / Suguna, K. / Surolia, A. / Vijayan, M. #2: Journal: Curr.Sci. / Year: 1997 Title: The Specificity of Peanut Agglutinin for Thomsen-Friedenreich Antigen is Mediated by Water-Bridges Authors: Ravishankar, R. / Ravindran, M. / Suguna, K. / Surolia, A. / Vijayan, M. #3: Journal: J.Mol.Biol. / Year: 1996 Title: Conformation, Protein-Carbohydrate Interactions and a Novel Subunit Association in the Refined Structure of Peanut Lectin-Lactose Complex Authors: Banerjee, R. / Das, K. / Ravishankar, R. / Suguna, K. / Surolia, A. / Vijayan, M. #4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994 Title: Crystal Structure of Peanut Lectin, a Protein with an Unusual Quaternary Structure Authors: Banerjee, R. / Mande, S.C. / Ganesh, V. / Das, K. / Dhanaraj, V. / Mahanta, S.K. / Suguna, K. / Surolia, A. / Vijayan, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cr7.cif.gz | 363.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cr7.ent.gz | 296.1 KB | Display | PDB format |
PDBx/mmJSON format | 1cr7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cr/1cr7 ftp://data.pdbj.org/pub/pdb/validation_reports/cr/1cr7 | HTTPS FTP |
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-Related structure data
Related structure data | 1cq9C 2pelS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Details | THERE ARE TWO TETRAMERS IN THE ASYMMETRIC UNIT WITHOUT 222 OR FOUR-FOLD SYMMETRY. CHAINS A,B,C AND D FORM ONE TETRAMER WHILE CHAINS E,F,G AND H FORM THE OTHER INDEPENDENT TETRAMER |
-Components
#1: Protein | Mass: 25208.955 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Arachis hypogaea (peanut) / References: PIR: S14765, UniProt: P02872*PLUS #2: Polysaccharide | #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-MN / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.32 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: small tubes / pH: 4.6 Details: PURE PROTEIN EXTENSIVELY DIALYSED AGAINST SODIUM ACETATE BUFFER AT PH 4.6 WAS USED IN THE CRYSTALLIZATION TRIALS. CRYSTALS WERE OBTAINED BY THE BATCH METHOD USING 4-5 MG/ML PROTEIN IN 0.05 M ...Details: PURE PROTEIN EXTENSIVELY DIALYSED AGAINST SODIUM ACETATE BUFFER AT PH 4.6 WAS USED IN THE CRYSTALLIZATION TRIALS. CRYSTALS WERE OBTAINED BY THE BATCH METHOD USING 4-5 MG/ML PROTEIN IN 0.05 M SODIUM ACETATE BUFFER CONTAINING 0.2 M SODIUM CHLORIDE, 1.5 MM LACTOSE AND 0.05 %SODIUM AZIDE. THE PRECIPITANT USED WAS PEG 8000, A SOLUTION OF WHICH IN THE SAME BUFFER WAS ADDED TO A FINAL CONCENTRATION OF ABOUT 12%. THE TUBES WERE LEFT UNDISTURBED FOR ABOUT TWO WEEKS, BY WHICH TIME CRYSTALS SUITABLE FOR DATA COLLECTION GREW., SMALL TUBES, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.4 / Method: microdialysis / Details: Salunke, D.M., (1983) FEBS Lett., 156, 127. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. obs: 65505 / % possible obs: 86.3 % / Redundancy: 4.75 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.134 |
Reflection | *PLUS Num. measured all: 311508 |
Reflection shell | *PLUS % possible obs: 68.4 % / Rmerge(I) obs: 0.316 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PEL Resolution: 2.6→10 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 Details: BULK SOLVENT MODEL USED. NCS CONSTRAINTS WERE APPLIED WITHIN EACH OF THE FOLLOWING GROUPS: SUBUNITS A, B, E; SUBUNITS C, G; SUBUNITS D, H
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Solvent computation | Solvent model: BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→10 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAIN | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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